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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI CTP SYNTHETASE
 
Authors :  J. A. Endrizzi, H. Kim, P. M. Anderson, E. P. Baldwin
Date :  06 Jan 04  (Deposition) - 15 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Ctp Synthetase, Utp:Ammonia Ligase (Adp-Forming), Cytidine 5'- Triphosphate Synthase, Ammonia Lyase, Class-Ii Glutamine Amidotransferase, Ammonia Tunnel, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Endrizzi, H. Kim, P. M. Anderson, E. P. Baldwin
Crystal Structure Of Escherichia Coli Cytidine Triphosphate Synthetase, A Nucleotide-Regulated Glutamine Amidotransferase/Atp-Dependent Amidoligase Fusion Protein And Homologue Of Anticancer And Antiparasitic Drug Targets
Biochemistry V. 43 6447 2004
PubMed-ID: 15157079  |  Reference-DOI: 10.1021/BI0496945

(-) Compounds

Molecule 1 - CTP SYNTHASE
    Chains: A, B
    EC Number: 6.3.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYRG, B2780, C3345, Z4095, ECS3640, SF2795, S2989
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: UTP--AMMONIA LIGASE, CTP SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1IOD16Ligand/IonIODIDE ION
2MG4Ligand/IonMAGNESIUM ION
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 44)
No.NameCountTypeFull Name
1IOD32Ligand/IonIODIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4SO48Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:15 , GLY A:17 , LYS A:18 , GLY A:19 , SO4 A:603 , MG A:702 , HOH A:908 , HOH A:970BINDING SITE FOR RESIDUE SO4 A 602
02AC2SOFTWARELYS A:18 , LYS A:40 , GLU A:140 , GLY A:142 , GLY A:143 , SO4 A:602 , MG A:702 , MG A:703 , HOH A:872BINDING SITE FOR RESIDUE SO4 A 603
03AC3SOFTWARESER B:15 , LEU B:16 , GLY B:17 , LYS B:18 , GLY B:19 , MG B:701 , HOH B:1688 , HOH B:1690BINDING SITE FOR RESIDUE SO4 B 1602
04AC4SOFTWARELYS B:18 , LYS B:40 , GLY B:142 , GLY B:143 , MG B:701 , MG B:704BINDING SITE FOR RESIDUE SO4 B 1603
05AC5SOFTWAREGLY B:19 , ASP B:72 , GLU B:140 , SO4 B:1602 , SO4 B:1603BINDING SITE FOR RESIDUE MG B 701
06AC6SOFTWAREGLY A:19 , LYS A:40 , ASP A:72 , GLU A:140 , SO4 A:602 , SO4 A:603BINDING SITE FOR RESIDUE MG A 702
07AC7SOFTWARELYS A:40 , ASP A:42 , PRO A:43 , SO4 A:603BINDING SITE FOR RESIDUE MG A 703
08AC8SOFTWARELYS B:40 , ASP B:42 , SO4 B:1603BINDING SITE FOR RESIDUE MG B 704
09AC9SOFTWARESER A:237 , LYS A:239BINDING SITE FOR RESIDUE IOD A 801
10BC1SOFTWARESER B:237 , LYS B:239BINDING SITE FOR RESIDUE IOD B 802
11BC2SOFTWAREGLU B:163BINDING SITE FOR RESIDUE IOD B 804
12BC3SOFTWARELYS A:233 , LYS A:262BINDING SITE FOR RESIDUE IOD A 805
13BC4SOFTWAREPRO A:178 , PRO B:178BINDING SITE FOR RESIDUE IOD A 806
14BC5SOFTWAREHOH A:979BINDING SITE FOR RESIDUE IOD A 807
15BC6SOFTWARELYS B:189 , HOH B:1754BINDING SITE FOR RESIDUE IOD B 808
16BC7SOFTWAREVAL B:241 , ASP B:242BINDING SITE FOR RESIDUE IOD B 810
17BC8SOFTWAREHOH B:1871BINDING SITE FOR RESIDUE IOD B 811
18BC9SOFTWAREVAL A:241 , ASP A:242BINDING SITE FOR RESIDUE IOD A 812
19CC1SOFTWAREGLU A:64 , VAL A:464 , ARG A:466BINDING SITE FOR RESIDUE IOD A 813
20CC2SOFTWAREHIS A:193 , HIS B:193 , HOH B:1735BINDING SITE FOR RESIDUE IOD A 814
21CC3SOFTWAREARG B:466 , HOH B:1774BINDING SITE FOR RESIDUE IOD B 815
22CC4SOFTWAREHIS B:193BINDING SITE FOR RESIDUE IOD A 816
23CC5SOFTWAREARG A:211 , LYS A:239 , ASP A:240 , VAL A:241 , ILE A:244 , ALA B:182BINDING SITE FOR RESIDUE MPD A 601
24CC6SOFTWAREARG B:211 , LEU B:238 , LYS B:239BINDING SITE FOR RESIDUE MPD B 1601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S1M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:116 -Pro A:117
2Ile B:116 -Pro B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S1M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S1M)

(-) Exons   (0, 0)

(no "Exon" information available for 1S1M)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:534
 aligned with PYRG_ECOLI | P0A7E5 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:544
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540    
           PYRG_ECOLI     1 MTTNYIFVTGGVVSSLGKGIAAASLAAILEARGLNVTIMKLDPYINVDPGTMSPIQHGEVFVTEDGAETDLDLGHYERFIRTKMSRRNNFTTGRIYSDVLRKERRGDYLGATVQVIPHITNAIKERVLEGGEGHDVVLVEIGGTVGDIESLPFLEAIRQMAVEIGREHTLFMHLTLVPYMAASGEVKTKPTQHSVKELLSIGIQPDILICRSDRAVPANERAKIALFCNVPEKAVISLKDVDSIYKIPGLLKSQGLDDYICKRFSLNCPEANLSEWEQVIFEEANPVSEVTIGMVGKYIELPDAYKSVIEALKHGGLKNRVSVNIKLIDSQDVETRGVEILKGLDAILVPGGFGYRGVEGMITTARFARENNIPYLGICLGMQVALIDYARHVANMENANSTEFVPDCKYPVVALITEWRDENGNVEVRSEKSDLGGTMRLGAQQCQLVDDSLVRQLYNAPTIVERHRHRYEVNNMLLKQIEDAGLRVAGRSGDDQLVEIIEVPNHPWFVACQFHPEFTSTPRDGHPLFAGFVKAASEFQKRQA 544
               SCOP domains d1s1ma2 A:1-266 CTP synthase PyrG, N-terminal domain                                                                                                                                                                                                                      --------------------d1s1ma1 A:287-544 CTP synthase PyrG, C-terminal domain                                                                                                                                                                                                             SCOP domains
               CATH domains 1s1mA01 A:1-285 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                         1s1mA02 A:286-544  [code=3.40.50.880, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhh....eeeeeee.....hhhhh........ee.....ee.hhhhhhhhhh....hhh.eeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh...eeeeeeee..ee....ee.hhhhhhhhhhhhh......eeeeee....hhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhh........eeee.......hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh....ee.........eeee.............----------..eeeeeeeee...hhhhhhh...eeeeeeee..eehhhhhhhhhhh..eeeee......eeeee......eeee..hhhhh......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s1m A   1 MTTNYIFVTGGVVSSLGKGIAAASLAAILEARGLNVTIMKLDPYINVDPGTMSPIQHGEVFVTEDGAETDLDLGHYERFIRTKMSRRNNFTTGRIYSDVLRKERRGDYLGATVQVIPHITNAIKERVLEGGEGHDVVLVEIGGTVGDIESLPFLEAIRQMAVEIGREHTLFMHLTLVPYMAASGEVKTKPTQHSVKELLSIGIQPDILICRSDRAVPANERAKIALFCNVPEKAVISLKDVDSIYKIPGLLKSQGLDDYICKRFSLNCPEANLSEWEQVIFEEANPVSEVTIGMVGKYIELPDAYKSVIEALKHGGLKNRVSVNIKLIDSQDVETRGVEILKGLDAILVPGGFGYRGVEGMITTARFARENNIPYLGICLGMQVALIDYARHVANMENANSTEFVPDCKYPVVALITEWRDENGNVE----------TMRLGAQQCQLVDDSLVRQLYNAPTIVERHRHRYEVNNMLLKQIEDAGLRVAGRSGDDQLVEIIEVPNHPWFVACQFHPEFTSTPRDGHPLFAGFVKAASEFQKRQA 544
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420      |  -       440       450       460       470       480       490       500       510       520       530       540    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    427        438                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:536
 aligned with PYRG_ECOLI | P0A7E5 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:545
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540     
           PYRG_ECOLI     1 MTTNYIFVTGGVVSSLGKGIAAASLAAILEARGLNVTIMKLDPYINVDPGTMSPIQHGEVFVTEDGAETDLDLGHYERFIRTKMSRRNNFTTGRIYSDVLRKERRGDYLGATVQVIPHITNAIKERVLEGGEGHDVVLVEIGGTVGDIESLPFLEAIRQMAVEIGREHTLFMHLTLVPYMAASGEVKTKPTQHSVKELLSIGIQPDILICRSDRAVPANERAKIALFCNVPEKAVISLKDVDSIYKIPGLLKSQGLDDYICKRFSLNCPEANLSEWEQVIFEEANPVSEVTIGMVGKYIELPDAYKSVIEALKHGGLKNRVSVNIKLIDSQDVETRGVEILKGLDAILVPGGFGYRGVEGMITTARFARENNIPYLGICLGMQVALIDYARHVANMENANSTEFVPDCKYPVVALITEWRDENGNVEVRSEKSDLGGTMRLGAQQCQLVDDSLVRQLYNAPTIVERHRHRYEVNNMLLKQIEDAGLRVAGRSGDDQLVEIIEVPNHPWFVACQFHPEFTSTPRDGHPLFAGFVKAASEFQKRQAK 545
               SCOP domains d1s1mb2 B:1-266 CTP synthase PyrG, N-terminal domain                                                                                                                                                                                                                      --------------------d1s1mb1 B:287-545 CTP synthase PyrG, C-terminal domain                                                                                                                                                                                                              SCOP domains
               CATH domains 1s1mB01 B:1-285 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                         1s1mB02 B:286-545  [code=3.40.50.880, no name defined]                                                                                                                                                                                                               CATH domains
           Pfam domains (1) --CTP_synth_N-1s1mB03 B:3-276                                                                                                                                                                                                                                                       -----------------------GATase-1s1mB01 B:300-535                                                                                                                                                                                                                    ---------- Pfam domains (1)
           Pfam domains (2) --CTP_synth_N-1s1mB04 B:3-276                                                                                                                                                                                                                                                       -----------------------GATase-1s1mB02 B:300-535                                                                                                                                                                                                                    ---------- Pfam domains (2)
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh..ee.....ee.hhhhhhhh......hhh.eeehhhhhhhhhhhhh............hhhhhhhhhhhhhhhh...eeeeeeeee.....hhhhhhhhhhhhhhhh...eeeeeeee...........hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeeehhhhhhhh........eeee.......hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh.....ee.........eeeehhhhh.........---------..eeeeeeeee...hhhhhhh...eeeeeeee..ee...hhhhhhh...eeeeee....eeeeee......eeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s1m B   1 MTTNYIFVTGGVVSSLGKGIAAASLAAILEARGLNVTIMKLDPYINVDPGTMSPIQHGEVFVTEDGAETDLDLGHYERFIRTKMSRRNNFTTGRIYSDVLRKERRGDYLGATVQVIPHITNAIKERVLEGGEGHDVVLVEIGGTVGDIESLPFLEAIRQMAVEIGREHTLFMHLTLVPYMAASGEVKTKPTQHSVKELLSIGIQPDILICRSDRAVPANERAKIALFCNVPEKAVISLKDVDSIYKIPGLLKSQGLDDYICKRFSLNCPEANLSEWEQVIFEEANPVSEVTIGMVGKYIELPDAYKSVIEALKHGGLKNRVSVNIKLIDSQDVETRGVEILKGLDAILVPGGFGYRGVEGMITTARFARENNIPYLGICLGMQVALIDYARHVANMENANSTEFVPDCKYPVVALITEWRDENGNVEV---------TMRLGAQQCQLVDDSLVRQLYNAPTIVERHRHRYEVNNMLLKQIEDAGLRVAGRSGDDQLVEIIEVPNHPWFVACQFHPEFTSTPRDGHPLFAGFVKAASEFQKRQAK 545
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       | -       440       450       460       470       480       490       500       510       520       530       540     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     428       438
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Glutaminase_I (73)
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PYRG_ECOLI | P0A7E5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003883    CTP synthase activity    Catalysis of the reaction: ATP + UTP + NH3 = ADP + phosphate + CTP.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0044210    'de novo' CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of cytidine 5'-triphosphate (CTP) from simpler components.
    GO:0006241    CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PYRG_ECOLI | P0A7E5: 2ad5 5tkv

(-) Related Entries Specified in the PDB File

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